added paralellization for windows to dist.seqs and summary.seqs

[mothur.git] / classifyseqscommand.h

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index 115360f7d5c3015130b0beef8a704f7669a382b5..3dbf06ee5bf18c5f6c5ee96e717ec4348c919310 100644 (file)
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -13,6 +13,7 @@
 #include "mothur.h"
 #include "command.hpp"
 #include "classify.h"
+#include "referencedb.h"
 
 //KNN and Bayesian methods modeled from algorithms in
 //Naı¨ve Bayesian Classifier for Rapid Assignment of rRNA Sequences 
@@ -35,6 +36,8 @@ public:
        string getCommandName()                 { return "classify.seqs";               }
        string getCommandCategory()             { return "Phylotype Analysis";  }
        string getHelpString(); 
+       string getCitation() { return "Wang Q, Garrity GM, Tiedje JM, Cole JR (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-7. [ for Bayesian classifier ] \nAltschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-402. [ for BLAST ] \nDeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-72. [ for kmer ] \nhttp://www.mothur.org/wiki/Classify.seqs"; }
+       string getDescription()         { return "classify sequences"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
@@ -58,11 +61,12 @@ private:
        map<string,  vector<string> >::iterator itNames;
        
        Classify* classify;
+       ReferenceDB* rdb;
        
        string fastaFileName, templateFileName, distanceFileName, namefile, search, method, taxonomyFileName, outputDir, groupfile;
        int processors, kmerSize, numWanted, cutoff, iters;
        float match, misMatch, gapOpen, gapExtend;
-       bool abort, probs;
+       bool abort, probs, save;
        
        int driver(linePair*, string, string, string);
        void appendTaxFiles(string, string);